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Posted to commits@airavata.apache.org by la...@apache.org on 2014/04/28 18:12:19 UTC
[6/9] seperate gfac-hadoop from gfac-core
http://git-wip-us.apache.org/repos/asf/airavata/blob/9a787309/modules/gfac/gfac-hadoop/src/test/resources/PBSTemplate.xslt
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diff --git a/modules/gfac/gfac-hadoop/src/test/resources/PBSTemplate.xslt b/modules/gfac/gfac-hadoop/src/test/resources/PBSTemplate.xslt
new file mode 100644
index 0000000..e749e9c
--- /dev/null
+++ b/modules/gfac/gfac-hadoop/src/test/resources/PBSTemplate.xslt
@@ -0,0 +1,73 @@
+<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under
+ the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance with the License. You may
+ obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to
+ in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF
+ ANY ~ KIND, either express or implied. See the License for the specific language governing permissions and limitations under
+ the License. -->
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
+<xsl:output method="text" />
+<xsl:template match="/ns:JobDescriptor">
+#! /bin/sh
+# PBS batch job script built by Globus job manager
+# <xsl:choose>
+ <xsl:when test="ns:shellName">
+##PBS -S <xsl:value-of select="ns:shellName"/>
+ </xsl:when></xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:queueName">
+#PBS -q <xsl:value-of select="ns:queueName"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:mailOptions">
+#PBS -m <xsl:value-of select="ns:mailOptions"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+<xsl:when test="ns:acountString">
+#PBS -A <xsl:value-of select="ns:acountString"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:maxWallTime">
+#PBS -l walltime=<xsl:value-of select="ns:maxWallTime"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#PBS -o <xsl:value-of select="ns:standardOutFile"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#PBS -e <xsl:value-of select="ns:standardErrorFile"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
+#PBS -l nodes=<xsl:value-of select="ns:nodes"/>:ppn=<xsl:value-of select="ns:processesPerNode"/>
+<xsl:text>
</xsl:text>
+ </xsl:when>
+ </xsl:choose>
+<xsl:for-each select="ns:exports/ns:name">
+<xsl:value-of select="."/>=<xsl:value-of select="./@value"/><xsl:text>
</xsl:text>
+export<xsl:text> </xsl:text><xsl:value-of select="."/>
+<xsl:text>
</xsl:text>
+</xsl:for-each>
+<xsl:for-each select="ns:preJobCommands/ns:command">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+ </xsl:for-each>
+cd <xsl:text> </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>
</xsl:text>
+ <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
+<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text> </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text> </xsl:text>
+<xsl:for-each select="ns:inputs/ns:input">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+ </xsl:for-each>
+<xsl:for-each select="ns:postJobCommands/ns:command">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+</xsl:for-each>
+
+</xsl:template>
+
+</xsl:stylesheet>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/9a787309/modules/gfac/gfac-hadoop/src/test/resources/gfac-config.xml
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diff --git a/modules/gfac/gfac-hadoop/src/test/resources/gfac-config.xml b/modules/gfac/gfac-hadoop/src/test/resources/gfac-config.xml
new file mode 100644
index 0000000..7c7e704
--- /dev/null
+++ b/modules/gfac/gfac-hadoop/src/test/resources/gfac-config.xml
@@ -0,0 +1,90 @@
+<!-- ~ Licensed to the Apache Software Foundation (ASF) under one ~ or more
+ contributor license agreements. See the NOTICE file ~ distributed with this
+ work for additional information ~ regarding copyright ownership. The ASF
+ licenses this file ~ to you under the Apache License, Version 2.0 (the ~
+ "License"); you may not use this file except in compliance ~ with the License.
+ You may obtain a copy of the License at ~ ~ http://www.apache.org/licenses/LICENSE-2.0
+ ~ ~ Unless required by applicable law or agreed to in writing, ~ software
+ distributed under the License is distributed on an ~ "AS IS" BASIS, WITHOUT
+ WARRANTIES OR CONDITIONS OF ANY ~ KIND, either express or implied. See the
+ License for the ~ specific language governing permissions and limitations
+ ~ under the License. -->
+
+<GFac>
+ <GlobalHandlers>
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.AppDescriptorCheckHandler">
+ <property name="name" value="value"/>
+ </Handler>
+ </InHandlers>
+ <OutHandlers></OutHandlers>
+ </GlobalHandlers>
+ <Provider class="org.apache.airavata.gfac.provider.impl.LocalProvider" host="org.apache.airavata.schemas.gfac.impl.HostDescriptionTypeImpl">
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.LocalDirectorySetupHandler"/>
+ </InHandlers>
+ </Provider>
+ <Provider class="org.apache.airavata.gfac.provider.impl.GramProvider" host="org.apache.airavata.schemas.gfac.impl.GlobusHostTypeImpl">
+ <property name="name" value="value"/>
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GramDirectorySetupHandler">
+ <property name="name" value="value"/>
+ </Handler>
+ <Handler class="org.apache.airavata.gfac.handler.GridFTPInputHandler"/>
+ </InHandlers>
+ <OutHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GridFTPOutputHandler"/>
+ </OutHandlers>
+ </Provider>
+ <Provider class="org.apache.airavata.gfac.provider.impl.BESProvider" host="org.apache.airavata.schemas.gfac.impl.UnicoreHostTypeImpl">
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GramDirectorySetupHandler"/>
+ <Handler class="org.apache.airavata.gfac.handler.GridFTPInputHandler"/>
+ </InHandlers>
+ <OutHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GridFTPOutputHandler"/>
+ </OutHandlers>
+ </Provider>
+
+ <Provider class="org.apache.airavata.gfac.ec2.EC2Provider" host="org.apache.airavata.schemas.gfac.impl.Ec2HostTypeImpl">
+ <InHandlers/>
+ <OutHandlers/>
+ </Provider>
+
+ <Provider class="org.apache.airavata.gfac.provider.impl.HadoopProvider" host="org.apache.airavata.schemas.gfac.impl.HadoopHostTypeImpl">
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.HadoopDeploymentHandler"/>
+ <Handler class="org.apache.airavata.gfac.handler.HDFSDataMovementHandler"/>
+ </InHandlers>
+ <OutHandlers/>
+ </Provider>
+
+ <Application name="UltraScan">
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GramDirectorySetupHandler"/>
+ <Handler class="org.apache.airavata.gfac.handler.GridFTPInputHandler"/>
+ </InHandlers>
+ <OutHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GridFTPOutputHandler"/>
+ </OutHandlers>
+ </Application>
+
+ <Provider class="org.apache.airavata.gfac.provider.impl.SSHProvider" host="org.apache.airavata.schemas.gfac.impl.SSHHostTypeImpl">
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.SSHDirectorySetupHandler"/>
+ <Handler class="org.apache.airavata.gfac.handler.GSISSHInputHandler"/>
+ </InHandlers>
+ <OutHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GSISSHOutputHandler"/>
+ </OutHandlers>
+ </Provider>
+ <Provider class="org.apache.airavata.gfac.provider.impl.GSISSHProvider" host="org.apache.airavata.schemas.gfac.impl.GsisshHostTypeImpl">
+ <InHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GSISSHDirectorySetupHandler"/>
+ <Handler class="org.apache.airavata.gfac.handler.GSISSHInputHandler"/>
+ </InHandlers>
+ <OutHandlers>
+ <Handler class="org.apache.airavata.gfac.handler.GSISSHOutputHandler"/>
+ </OutHandlers>
+ </Provider>
+</GFac>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/9a787309/modules/gfac/gfac-hadoop/src/test/resources/logging.properties
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diff --git a/modules/gfac/gfac-hadoop/src/test/resources/logging.properties b/modules/gfac/gfac-hadoop/src/test/resources/logging.properties
new file mode 100644
index 0000000..0584d38
--- /dev/null
+++ b/modules/gfac/gfac-hadoop/src/test/resources/logging.properties
@@ -0,0 +1,42 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#
+#default/fallback log4j configuration
+#
+
+# Set root logger level to WARN and its only appender to A1.
+log4j.rootLogger=INFO, A1, A2
+
+# A1 is set to be a rolling file appender with default params
+log4j.appender.A1=org.apache.log4j.RollingFileAppender
+log4j.appender.A1.File=target/seclogs.txt
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%d [%t] %-5p %c %x - %m%n
+
+# A2 is a console appender
+log4j.appender.A2=org.apache.log4j.ConsoleAppender
+
+# A2 uses PatternLayout.
+log4j.appender.A2.layout=org.apache.log4j.PatternLayout
+log4j.appender.A2.layout.ConversionPattern=%d [%t] %-5p %c{1} %x - %m%n
+
+log4j.logger.unicore.security=INFO
+
http://git-wip-us.apache.org/repos/asf/airavata/blob/9a787309/modules/gfac/gfac-ssh/pom.xml
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diff --git a/modules/gfac/gfac-ssh/pom.xml b/modules/gfac/gfac-ssh/pom.xml
index c463661..6d15355 100644
--- a/modules/gfac/gfac-ssh/pom.xml
+++ b/modules/gfac/gfac-ssh/pom.xml
@@ -103,6 +103,11 @@
<artifactId>xmlbeans</artifactId>
<version>${xmlbeans.version}</version>
</dependency>
+ <dependency>
+ <groupId>net.schmizz</groupId>
+ <artifactId>sshj</artifactId>
+ <version>0.6.1</version>
+ </dependency>
</dependencies>
http://git-wip-us.apache.org/repos/asf/airavata/blob/9a787309/modules/gfac/pom.xml
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diff --git a/modules/gfac/pom.xml b/modules/gfac/pom.xml
index d2ee2a5..774a445 100644
--- a/modules/gfac/pom.xml
+++ b/modules/gfac/pom.xml
@@ -34,7 +34,8 @@
<module>gfac-ec2</module>
<module>gfac-ssh</module>
<module>gfac-local</module>
- <module>gfac-gram</module>
+ <module>gfac-hadoop</module>
+ <module>gfac-gram</module>
<module>gfac-gsissh</module>
<module>gfac-bes</module>
</modules>